Resolving Cell Fate Decisions during Somatic Cell Reprogramming by Single-Cell RNA-Seq

Guo, Lin; Lin, Lihui; Wang, Xiaoshan; Gao, Mingwei; Cao, Shuiyan; Mai, Yuanbang; Wu, Fang; Kuang, Jinqiang; Liu, He; Yang, Jiaqi; Chu, Shilong; Sui, Hong; Li, Dongwei; Liu, Yujian; Wu, Kaixin; Liu, Jiadong; Wang, Jinyong; Pan, Guangjin; Hutchins, Andrew P.; Liu, Jing; Pei, Duanqing; Chen, Jiekai

doi:10.1016/j.molcel.2019.01.042

Cited by 94 publications

(72 citation statements)

References 77 publications

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“…Finally, Transient KLF4 targets enriched for enhancers previously detected in partially reprogrammed cells 8 (Supplementary Fig.1b) as well as genes involved in negative regulation of cell cycle, apoptosis and various signaling pathways associated with differentiation, such as TGF-beta signaling (Fig.1c). Therefore, transient KLF4 binding might be associated with unsuccessful reprogramming and alternative fates induced by OKSM expression, as reported in other studies 31–33 .…”

Section: Resultssupporting

confidence: 61%

KLF4 binding is involved in the organization and regulation of 3D enhancer networks during acquisition and maintenance of pluripotency

Giammartino

Kloetgen

Polyzos

et al. 2018

Preprint

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SUMMARY 28Cell fate transitions are accompanied by global transcriptional, epigenetic and 29 topological changes driven by transcription factors (TFs), as is strikingly 30 exemplified in somatic cell reprogramming to pluripotent stem cells (PSCs) by 31 OCT4, KLF4, SOX2 and cMYC. How TFs orchestrate the complex molecular 32 changes around their targets in a temporal manner remains largely elusive. Here, 33 using KLF4 as a paradigm, we provide the first TF-centric view of chromatin 34 reorganization during reprogramming and its association to enhancer rewiring 35 and gene regulation. We captured the enhancer connectomes in fibroblasts and 36PSCs by H3K27ac HiChIP and identified complex 3D enhancer hubs that were 37 strongly correlated with cell-type specific gene expression and coregulation. 38 KLF4-centric conformational analysis at different reprogramming stages revealed 39that KLF4 is involved in the dissociation of fibroblast-specific and the 40 establishment of PSC-specific enhancer loops concomitantly with repression or 41 activation of linked genes. Moreover, KLF4 occupancy was significantly enriched 42 within highly connected enhancers, suggesting a role in the formation and 43 regulation of complex enhancer hubs. Indeed, disruption of a single KLF4 binding 44 site from a PSC-specific enhancer was sufficient to reduce expression of multiple 45 genes within the enhancer hub, partly by impairing long-range contact. Our study 46 provides an integrative view of the intricate activities of a master regulator during 47 a controlled cell fate transition and offers novel insights into the order and nature 48 of molecular events that follow TF binding.

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Section: Resultssupporting

confidence: 61%

KLF4 binding is involved in the organization and regulation of 3D enhancer networks during acquisition and maintenance of pluripotency

Giammartino

Kloetgen

Polyzos

et al. 2018

Preprint

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“…Since Cell Ranger is widely used, we investigated the extent to which the Cell Ranger results are concordant with our workflow. We processed 20 datasets ( Supplementary Table 1), chosen to contain a range of reads depths (from 8,860,361 to 721,180,737 reads per sample and 2,243 to 201,952 reads per cell) and to represent scRNA-seq from a range of tissues and species ( Arabidopsis thaliania 18 , Caenorhabditis elegans 19 , Danio rerio 20 , Drosophila melanogaster 21 , Homo sapiens 22,23 , Mus musculus [24][25][26][27][28] , Rattus norvegicus 28 ). We found a high degree of concordance with respect to quality control metrics (Figure 2a-h, Supplementary Figure 3).…”

Section: Resultsmentioning

confidence: 99%

Modular and efficient pre-processing of single-cell RNA-seq

Melsted

Booeshaghi

Gao

et al. 2019

Preprint

102

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Analysis of single-cell RNA-seq data begins with the pre-processing of reads to generate count matrices. We investigate algorithm choices for the challenges of pre-processing, and describe a workflow that balances efficiency and accuracy. Our workflow is based on the kallisto and bustools programs, and is near-optimal in speed and memory. The workflow is modular, and we demonstrate its flexibility by showing how it can be used for RNA velocity analyses.

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“…5 A more recent method, uniform manifold approximation (UMAP), estimates a topology of the high dimensional data and uses this information to construct a low-dimensional representation that preserves relationships present in the data. 6 UMAP has been particularly useful to precisely define cell types in mixed populations based on data from single-cell RNA-seq experiments [7][8][9][10][11][12][13] ; it also performs well on other goldstandard datasets. 6,14 Because UMAP is better able to preserve elements of the data structure from high dimensional space than similar outputs from t-SNE, it captures local relationships within distinct clusters in addition to global relationships between clusters.…”

mentioning

confidence: 99%

Dimensionality reduction by UMAP to visualize physical and genetic interactions

Dorrity

Saunders

Queitsch

et al. 2019

Preprint

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Dimensionality reduction is often used to visualize complex expression profilingdata. Here, we use the Uniform Manifold Approximation and Projection (UMAP) method on published transcript profiles of 1484 single gene deletions of Saccharomyces cerevisiae. Proximity in low-dimensional UMAP space identifies clusters of genes that correspond to protein complexes and pathways, and finds novel protein interactions even within well-characterized complexes. This approach is more sensitive than previous methods and should be broadly useful as additional transcriptome datasets become available for other organisms.A central goal of biological studies is the identification and characterization of proteins that act in a common cellular pathway. Efforts towards this goal have been greatly aided by large-scale perturbation analyses coupled with whole-transcriptome profiling, in which each gene's transcriptional response to a perturbation is measured. If a sufficient database of expression profiles exists, then a pathway affected by an uncharacterized

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Resolving Cell Fate Decisions during Somatic Cell Reprogramming by Single-Cell RNA-Seq

Cited by 94 publications

References 77 publications

KLF4 binding is involved in the organization and regulation of 3D enhancer networks during acquisition and maintenance of pluripotency

KLF4 binding is involved in the organization and regulation of 3D enhancer networks during acquisition and maintenance of pluripotency

Modular and efficient pre-processing of single-cell RNA-seq

Dimensionality reduction by UMAP to visualize physical and genetic interactions

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